Genomic Characterization of Dengue Virus Outbreak in 2022 from Pakistan

Abstract

Pakistan, a dengue-endemic country, has encountered several outbreaks during the past decade. The current study aimed to explore the serotype and genomic diversity of dengue virus responsible for the 2022 outbreak in Pakistan. From August to October 2022, NS-1 positive blood samples (n = 343) were collected from dengue patients, among which, (85%; n = 293) were positive based on RT-PCR. In terms of gender and age, dengue infection was more prevalent in male patients (63%; n = 184), with more adults (21-30 years; n = 94) being infected. The serotyping results revealed DENV-2 to be the most predominant serotype (62%; n = 183), followed by DENV-1 (37%; n = 109) and DENV-3 (0.32%; n = 1). Moreover, a total of 10 samples (DENV-2; n = 8, DENV-1; n = 2) were subjected to whole-genome sequencing. Among these, four were collected in early 2022, and six were collected between August and October 2022. Phylogenetic analysis of DENV-2 sequenced samples (n = 8) revealed a monophyletic clade of cosmopolitan genotype IVA, which is closely related to sequences from China and Singapore 2018, and DENV-1 samples (n = 2) show genotype III, which is closely related to Pakistan isolates from 2019. We also reported the first whole genome sequence of a coinfection case (DENV1-DENV2) in Pakistan detected through a meta-genome approach. Thus, dengue virus dynamics reported in the current study warrant large-scale genomic surveillance to better respond to future outbreaks.

Keywords: DENV-1; DENV-2; coinfection; cosmopolitan genotype; dengue outbreak in Pakistan; serotype; whole genome sequencing.

Figure 1

Week-wise distribution of dengue virus serotypes (August–October 2022).

Figure 2

Geographical distribution of circulating dengue serotypes.

Figure 3

Maximum likelihood phylogenetic tree of dengue full genome sequences. The tree was generated through an IQ tree with 1000 bootstraps. The study isolates are highlighted in green, while the previously reported sequences of DENV from Pakistan are highlighted in yellow.

Figure 4

(A) Amino acid variation in the DENV2 study isolates in comparison with the reference strain and previously reported sequences from Pakistan. (B) Amino acid variation in the DENV1 study isolates in comparison with the reference strain and previously reported sequences from Pakistan. The amino acid differences are highlighted in red. X represents the missing amino acid at that position and dot (.) represents the same amino acid as present in the reference genome. * (AIU39216.1, AIU39217.1, AIU39218.1, AIE17400.1, AHM25909.1, AHC72404.1, AHC72406.1, AHC72407.1, AHC72405.1, AHM25910.1).